Soil microorganisms – fungi and bacteria

Soil microorganisms have a variety of beneficial roles, including nutrient cycling and mutualistic associations with plant roots (e.g. mycorrhizal fungi or rhizobia). However, some bacteria, fungi, or soilborne viruses can cause crop disease.

Back to: The function of soil biology

Beneficial microorganisms

Beneficial microorganisms include:

  • Decomposer organisms
  • Ectomycorrhizal fungi, that form a sheath around the plant root, extending the volume of soil that can be ‘tapped’ for nutrients
  • Arbuscular mycorrhizal fungi, which live within the root tissue and improve nutrient uptake for the plant (particularly phosphorus)
  • Nitrogen-fixing rhizobia, which associate with the roots of legumes and fix atmospheric nitrogen into a form that is useable by the plant
  • Plant growth-promoting rhizobacteria that colonise plant roots and can suppress plant disease, produce antibiotics, or improve nutrient acquisition
  • Microorganisms that are involved in biological control of plant pathogens, either through direct parasitism of the pathogen, competition for space or nutrients or production of antibiotics 

Defence responses to foliar pathogens can also be triggered by root-associated microorganisms. This is known as induced systemic resistance.

Soilborne plant pathogens and deleterious microorganisms

Soilborne pathogens may not cause obvious above-ground symptoms, although there may be stunting or areas of the field showing poor plant performance. Rotting roots will impair root functioning. Damage occurring below ground can have a significant impact, particularly when the harvested product is a root crop, as symptoms may not be noticed until harvest. 

Disease in the field can be patchy rather than uniform. Control of soilborne pathogens is not simple, and chemical options are not really viable. Spores of most soilborne pathogens can survive for many years. 

Microbial interactions in the root zone (rhizosphere) that have a detrimental effect on the plant without visible symptoms are not well understood. The impact of deleterious microorganisms on plant growth and productivity has been demonstrated by soil sterilisation or soil transfer experiments, and various modes of action have been implicated.

Microorganisms as biological indicators of soil health

Since bacteria and fungi are the dominant components of microbial biomass, it is often considered they provide the best indication of the soil’s biological status. However, they are difficult to measure as there are thousands of different species, they occur in enormous numbers and it is difficult to identify their function. Also, their life cycles are relatively short (hours or days), and so populations change rapidly in response to changes in environmental conditions such as moisture and temperature.

Useful links

Discover the soil food web

See how soil organisms stabilise soil structure

Learn about the different ecological groups of earthworms

Read about different ecological groups of nematodes

Find out more about Rhizoctonia solani symptoms and risk in oilseed rape

Learn more about clubroot in oilseed rape and field brassicas


Image of staff member Amanda Bennett

Amanda Bennett

Senior Environment Manager (Soil Health & RB209)

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